PXD055510 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Cysteine-directed isobaric labeling combined with GeLC-FAIMS MS for quantitative top-down proteomics |
Description | The quantification of proteoforms, i.e., all molecular forms in which proteins can be present, by top-down proteomics provides essential insights into biological processes at the molecular level. Isobaric labeling-based quantification strategies are suitable for multi-dimensional separation strategies and allow for multiplexing of the samples. Here, we investigated cysteine-directed isobaric labeling by iodoTMT in combination with a gel- and gas-phase fractionation (GeLC-FAIMS-MS) for in-depth quantitative proteoform analysis. We optimized the acquisition workflow (i.e., the FAIMS compensation voltages, isolation windows, acquisition strategy, and fragmentation method) using a two-proteome mix to increase the number of quantified proteoforms and reduce ratio compression. Additionally, we implemented a mass feature-based quantification strategy in the widely used deconvolution algorithm FLASHDeconv, which improves and facilitates data analysis. The optimized iodoTMT GeLC-FAIMS-MS workflow was applied to quantitatively analyze the proteome of Escherichia coli grown under glucose or acetate as the sole carbon source, resulting in the identification of 726 differentially abundant proteoforms. |
HostingRepository | PRIDE |
AnnounceDate | 2025-05-07 |
AnnouncementXML | Submission_2025-05-07_02:47:57.248.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Andreas Tholey |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932; |
ModificationList | cysTMT6plex reporter+balance reagent cysteine disulfide |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2024-09-03 04:19:34 | ID requested | |
⏵ 1 | 2025-05-07 02:47:58 | announced | |
Publication List
10.1021/acs.jproteome.4c00835; |
Matzanke T, Kaulich PT, Jeong K, Takemori A, Takemori N, Kohlbacher O, Tholey A, Cysteine-Directed Isobaric Labeling Combined with GeLC-FAIMS-MS for Quantitative Top-Down Proteomics. J Proteome Res, 24(3):1470-1480(2025) [pubmed] |
Keyword List
submitter keyword: Top-down proteomics |
TMT labeling |
quantitative proteomics |
FAIMS |
GeLC |
PEPPI |
Contact List
Andreas Tholey |
contact affiliation | Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine Christian-Albrechts-Universität zu Kiel 24105 Kiel, Germany |
contact email | a.tholey@iem.uni-kiel.de |
lab head | |
Andreas Tholey |
contact affiliation | Systematic Proteome Research & Bioanalytics, University of Kiel |
contact email | a.tholey@iem.uni-kiel.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD055510
- Label: PRIDE project
- Name: Cysteine-directed isobaric labeling combined with GeLC-FAIMS MS for quantitative top-down proteomics